OpenRaiser/Intern-Atlas huggingface dataset:
OMTRA: A Multi-Task Generative Model for Structure-Based Drug Design
Venue: arXiv cs.LG 2025
Year: 2025

Structure-based drug design (SBDD) focuses on designing small-molecule ligands that bind to specific protein pockets. Computational methods are integral in modern SBDD workflows and often make use of virtual screening methods via docking or pharmacophore search. Modern generative modeling approaches have focused on improving novel ligand discovery by enabling de novo design. In this work, we recognize that these tasks share a common structure and can therefore be represented as different instantiations of a consistent generative modeling framework. We propose a unified approach in OMTRA, a multi-modal flow matching model that flexibly performs many tasks relevant to SBDD, including some with no analogue in conventional workflows. Additionally, we curate a dataset of 500M 3D molecular conformers, complementing protein-ligand data and expanding the chemical diversity available for training. OMTRA obtains state of the art performance on pocket-conditioned de novo design and docking; however, the effects of large-scale pretraining and multi-task training are modest. All code, trained models, and dataset for reproducing this work are available at https://github.com/gnina/OMTRA
Visual Reasoning Tracer: Object-Level Grounded Reasoning Benchmark
Venue: arXiv cs.CV 2025
Year: 2025

Recent advances in Multimodal Large Language Models (MLLMs) have significantly improved performance on tasks such as visual grounding and visual question answering. However, the reasoning processes of these models remain largely opaque; they typically output only final predictions without revealing the intermediate steps or fine-grained evidence (e.g., pixels, locations) that lead to the result. This contrasts with human intelligence, which naturally operates through a chain of visual reasoning. To address this limitation, we introduce the Visual Reasoning Tracer (VRT) task, which requires models to not only localize the target object but also explicitly predict the intermediate objects that form the reasoning path. To advance research in this area, we contribute: (1) VRT-Bench, a human-annotated benchmark for evaluating visual reasoning; (2) a new metric for assessing the quality of reasoning traces; and (3) VRT-80k, a large-scale dataset for reasoning model training. Our experiments reveal that while existing models often produce the correct final output, they struggle to ground their intermediate reasoning. In contrast, models trained on VRT-80k achieve substantial improvements in tracing the reasoning path.
From Generated Human Videos to Physically Plausible Robot Trajectories
Venue: arXiv cs.RO 2025
Year: 2025

Video generation models are rapidly improving in their ability to synthesize human actions in novel contexts, holding the potential to serve as high-level planners for contextual robot control. To realize this potential, a key research question remains open: how can a humanoid execute the human actions from generated videos in a zero-shot manner? This challenge arises because generated videos are often noisy and exhibit morphological distortions that make direct imitation difficult compared to real video. To address this, we introduce a two-stage pipeline. First, we lift video pixels into a 4D human representation and then retarget to the humanoid morphology. Second, we propose GenMimic-a physics-aware reinforcement learning policy conditioned on 3D keypoints, and trained with symmetry regularization and keypoint-weighted tracking rewards. As a result, GenMimic can mimic human actions from noisy, generated videos. We curate GenMimicBench, a synthetic human-motion dataset generated using two video generation models across a spectrum of actions and contexts, establishing a benchmark for assessing zero-shot generalization and policy robustness. Extensive experiments demonstrate improvements over strong baselines in simulation and confirm coherent, physically stable motion tracking on a Unitree G1 humanoid robot without fine-tuning. This work offers a promising path to realizing the potential of video generation models as high-level policies for robot control.
EvoIR: Towards All-in-One Image Restoration via Evolutionary Frequency Modulation
Venue: arXiv cs.CV 2025
Year: 2025

All-in-One Image Restoration (AiOIR) tasks often involve diverse degradation that require robust and versatile strategies. However, most existing approaches typically lack explicit frequency modeling and rely on fixed or heuristic optimization schedules, which limit the generalization across heterogeneous degradation. To address these limitations, we propose EvoIR, an AiOIR-specific framework that introduces evolutionary frequency modulation for dynamic and adaptive image restoration. Specifically, EvoIR employs the Frequency-Modulated Module (FMM) that decomposes features into high- and low-frequency branches in an explicit manner and adaptively modulates them to enhance both structural fidelity and fine-grained details. Central to EvoIR, an Evolutionary Optimization Strategy (EOS) iteratively adjusts frequency-aware objectives through a population-based evolutionary process, dynamically balancing structural accuracy and perceptual fidelity. Its evolutionary guidance further mitigates gradient conflicts across degradation and accelerates convergence. By synergizing FMM and EOS, EvoIR yields greater improvements than using either component alone, underscoring their complementary roles. Extensive experiments on multiple benchmarks demonstrate that EvoIR outperforms state-of-the-art AiOIR methods.
ARM-Thinker: Reinforcing Multimodal Generative Reward Models with Agentic Tool Use and Visual Reasoning
Venue: arXiv cs.CV 2025
Year: 2025

Reward models are critical for aligning vision-language systems with human preferences, yet current approaches suffer from hallucination, weak visual grounding, and an inability to use tools for verification, limiting their reliability on complex multimodal reasoning tasks. We present ARM-Thinker, an A}gentic multimodal Reward Model that autonomously invokes external tools (e.g., image cropping, doc page retrieval) to ground judgments in verifiable evidence, replacing static, non-interactive reward scoring. This enables the model to verify fine-grained visual details, cross-reference multi-page evidence, and validate reasoning claims, which are capabilities absent in existing reward models. We train ARM-Thinker with multi-stage reinforcement learning, jointly optimizing tool-calling decisions and judgment accuracy. To evaluate agentic reward modeling, we introduce ARMBench-VL, comprising three benchmarks that assess fine-grained visual grounding (image-level tools), multi-page document understanding (retrieval tools), and instruction following (text-level verification). ARM-Thinker achieves +16.2% average improvement on reward modeling benchmarks, +9.6% on tool-use tasks, and outperforms baselines on multimodal math and logical reasoning benchmarks. Our results demonstrate that agentic capabilities significantly enhance both accuracy and interpretability of reward models.
Splannequin: Freezing Monocular Mannequin-Challenge Footage with Dual-Detection Splatting
Venue: arXiv cs.CV 2025
Year: 2025

Synthesizing high-fidelity frozen 3D scenes from monocular Mannequin-Challenge (MC) videos is a unique problem distinct from standard dynamic scene reconstruction. Instead of focusing on modeling motion, our goal is to create a frozen scene while strategically preserving subtle dynamics to enable user-controlled instant selection. To achieve this, we introduce a novel application of dynamic Gaussian splatting: the scene is modeled dynamically, which retains nearby temporal variation, and a static scene is rendered by fixing the model's time parameter. However, under this usage, monocular capture with sparse temporal supervision introduces artifacts like ghosting and blur for Gaussians that become unobserved or occluded at weakly supervised timestamps. We propose Splannequin, an architecture-agnostic regularization that detects two states of Gaussian primitives, hidden and defective, and applies temporal anchoring. Under predominantly forward camera motion, hidden states are anchored to their recent well-observed past states, while defective states are anchored to future states with stronger supervision. Our method integrates into existing dynamic Gaussian pipelines via simple loss terms, requires no architectural changes, and adds zero inference overhead. This results in markedly improved visual quality, enabling high-fidelity, user-selectable frozen-time renderings, validated by a 96% user preference. Project page: https://chien90190.github.io/splannequin/
Deep infant brain segmentation from multi-contrast MRI
Venue: arXiv cs.LG 2025
Year: 2025

Segmentation of magnetic resonance images (MRI) facilitates analysis of human brain development by delineating anatomical structures. However, in infants and young children, accurate segmentation is challenging due to development and imaging constraints. Pediatric brain MRI is notoriously difficult to acquire, with inconsistent availability of imaging modalities, substantial non-head anatomy in the field of view, and frequent motion artifacts. This has led to specialized segmentation models that are often limited to specific image types or narrow age groups, or that are fragile for more variable images such as those acquired clinically. We address this method fragmentation with BabySeg, a deep learning brain segmentation framework for infants and young children that supports diverse MRI protocols, including repeat scans and image types unavailable during training. Our approach builds on recent domain randomization techniques, which synthesize training images far beyond realistic bounds to promote dataset shift invariance. We also describe a mechanism that enables models to flexibly pool and interact features from any number of input scans. We demonstrate state-of-the-art performance that matches or exceeds the accuracy of several existing methods for various age cohorts and input configurations using a single model, in a fraction of the runtime required by many existing tools.
Documenting SME Processes with Conversational AI: From Tacit Knowledge to BPMN
Venue: arXiv cs.AI 2025
Year: 2025

Small and medium-sized enterprises (SMEs) still depend heavily on tacit, experience-based know-how that rarely makes its way into formal documentation. This paper introduces a large-language-model (LLM)-driven conversational assistant that captures such knowledge on the shop floor and converts it incrementally and interactively into standards-compliant Business Process Model and Notation (BPMN) 2.0 diagrams. Powered by Gemini 2.5 Pro and delivered through a lightweight Gradio front-end with client-side bpmn-js visualisation, the assistant conducts an interview-style dialogue: it elicits process details, supports clarifying dialogue and on-demand analysis, and renders live diagrams that users can refine in real time. A proof-of-concept evaluation in an equipment-maintenance scenario shows that the chatbot produced an accurate "AS-IS" model, flagged issues via on-diagram annotations, and generated an improved "TO-BE" variant, all within about 12-minutes, while keeping API costs within an SME-friendly budget. The study analyses latency sources, model-selection trade-offs, and the challenges of enforcing strict XML schemas, then outlines a roadmap toward agentic and multimodal deployments. The results demonstrate that conversational LLMs can potentially be used to lower the skill and cost barriers to rigorous process documentation, helping SMEs preserve institutional knowledge, enhance operational transparency, and accelerate continuous-improvement efforts.
Self-Improving VLM Judges Without Human Annotations
Venue: arXiv cs.CV 2025
Year: 2025

Effective judges of Vision-Language Models (VLMs) are crucial for model development. Current methods for training VLM judges mainly rely on large-scale human preference annotations. However, such an approach is costly, and the annotations easily become obsolete as models rapidly improve. In this work, we present a framework to self-train a VLM judge model without any human preference annotations, using only self-synthesized data. Our method is iterative and has three stages: (1) generate diverse multimodal instruction-response pairs at varying quality levels, (2) generate reasoning traces and judgments for each pair, removing the ones that do not match our expected quality levels, and (3) training on correct judge answers and their reasoning traces. We evaluate the resulting judge on Multimodal RewardBench and VL-RewardBench across domains: correctness, preference, reasoning, safety, and visual question-answering. Our method improves a Llama-3.2-11B multimodal judge from 0.38 to 0.51 in overall accuracy on VL-RewardBench, often outperforming much larger models including Llama-3.2-90B, GPT-4o, and Claude 3.5 Sonnet, with particularly strong gains in general, hallucination, and reasoning dimensions. The overall strength of these human-annotation-free results suggest the potential for a future self-judge that evolves alongside rapidly improving VLM capabilities.
Bridging Traditional Machine Learning and Large Language Models: A Two-Part Course Design for Modern AI Education
Venue: arXiv cs.AI 2025
Year: 2025

This paper presents an innovative pedagogical approach for teaching artificial intelligence and data science that systematically bridges traditional machine learning techniques with modern Large Language Models (LLMs). We describe a course structured in two sequential and complementary parts: foundational machine learning concepts and contemporary LLM applications. This design enables students to develop a comprehensive understanding of AI evolution while building practical skills with both established and cutting-edge technologies. We detail the course architecture, implementation strategies, assessment methods, and learning outcomes from our summer course delivery spanning two seven-week terms. Our findings demonstrate that this integrated approach enhances student comprehension of the AI landscape and better prepares them for industry demands in the rapidly evolving field of artificial intelligence.
Advanced Unsupervised Learning: A Comprehensive Overview of Multi-View Clustering Techniques
Venue: arXiv cs.LG 2025
Year: 2025

Machine learning techniques face numerous challenges to achieve optimal performance. These include computational constraints, the limitations of single-view learning algorithms and the complexity of processing large datasets from different domains, sources or views. In this context, multi-view clustering (MVC), a class of unsupervised multi-view learning, emerges as a powerful approach to overcome these challenges. MVC compensates for the shortcomings of single-view methods and provides a richer data representation and effective solutions for a variety of unsupervised learning tasks. In contrast to traditional single-view approaches, the semantically rich nature of multi-view data increases its practical utility despite its inherent complexity. This survey makes a threefold contribution: (1) a systematic categorization of multi-view clustering methods into well-defined groups, including co-training, co-regularization, subspace, deep learning, kernel-based, anchor-based, and graph-based strategies; (2) an in-depth analysis of their respective strengths, weaknesses, and practical challenges, such as scalability and incomplete data; and (3) a forward-looking discussion of emerging trends, interdisciplinary applications, and future directions in MVC research. This study represents an extensive workload, encompassing the review of over 140 foundational and recent publications, the development of comparative insights on integration strategies such as early fusion, late fusion, and joint learning, and the structured investigation of practical use cases in the areas of healthcare, multimedia, and social network analysis. By integrating these efforts, this work aims to fill existing gaps in MVC research and provide actionable insights for the advancement of the field.
Integrating Wearable Data into Process Mining: Event, Case and Activity Enrichment
Venue: arXiv cs.DB 2025
Year: 2025

In this short paper, we explore the enrichment of event logs with data from wearable devices. We discuss three approaches: (1) treating wearable data as event attributes, linking them directly to individual events, (2) treating wearable data as case attributes, using aggregated day-level scores, and (3) introducing new events derived from wearable data, such as sleep episodes or physical activities. To illustrate these approaches, we use real-world data from one person, matching health data from a smartwatch with events extracted from a digital calendar application. Finally, we discuss the technical and conceptual challenges involved in integrating wearable data into process mining for personal productivity and well-being.
NVLang: Unified Static Typing for Actor-Based Concurrency on the BEAM
Venue: arXiv cs.PL 2025
Year: 2025

Actor-based systems like Erlang/OTP power critical infrastructure -- from telecommunications to messaging platforms -- handling millions of concurrent connections with legendary reliability. Yet these systems lack static guarantees about message protocols: processes communicate by sending arbitrary messages that pattern-matched at runtime, deferring protocol violations to production failures. We present NVLang, a statically typed functional language that brings comprehensive type safety to the BEAM virtual machine while preserving actor model's simplicity and power. NVLang's central contribution that algebraic data types (ADTs) naturally encode actor message protocols: each actor declares the sum type representing its message vocabulary, and the type system enforces protocol conformance at compile time. We introduce typed process identifiers (Pid[T]) that encode the protocol an actor expects, and typed futures (Future[T]) that provide type-safe request-reply patterns. By extending Hindley-Milner type inference to track message protocols, NVLang eliminates an entire class of message-passing errors while maintaining clean syntax that rivals dynamically typed alternatives. Our implementation compiles to Core Erlang, enabling seamless interoperability with the existing Erlang ecosystem. We formalize the type system and provide proof sketches for type soundness, demonstrating that well-typed NVLang programs cannot send messages that violate actor protocols.
Enhancing Clinical Note Generation with ICD-10, Clinical Ontology Knowledge Graphs, and Chain-of-Thought Prompting Using GPT-4
Venue: arXiv cs.CL 2025
Year: 2025

In the past decade a surge in the amount of electronic health record (EHR) data in the United States, attributed to a favorable policy environment created by the Health Information Technology for Economic and Clinical Health (HITECH) Act of 2009 and the 21st Century Cures Act of 2016. Clinical notes for patients' assessments, diagnoses, and treatments are captured in these EHRs in free-form text by physicians, who spend a considerable amount of time entering and editing them. Manually writing clinical notes takes a considerable amount of a doctor's valuable time, increasing the patient's waiting time and possibly delaying diagnoses. Large language models (LLMs) possess the ability to generate news articles that closely resemble human-written ones. We investigate the usage of Chain-of-Thought (CoT) prompt engineering to improve the LLM's response in clinical note generation. In our prompts, we use as input International Classification of Diseases (ICD) codes and basic patient information. We investigate a strategy that combines the traditional CoT with semantic search results to improve the quality of generated clinical notes. Additionally, we infuse a knowledge graph (KG) built from clinical ontology to further enrich the domain-specific knowledge of generated clinical notes. We test our prompting technique on six clinical cases from the CodiEsp test dataset using GPT-4 and our results show that it outperformed the clinical notes generated by standard one-shot prompts.
Uncertainty-Aware Data-Efficient AI: An Information-Theoretic Perspective
Venue: arXiv cs.IT 2025
Year: 2025

In context-specific applications such as robotics, telecommunications, and healthcare, artificial intelligence systems often face the challenge of limited training data. This scarcity introduces epistemic uncertainty, i.e., reducible uncertainty stemming from incomplete knowledge of the underlying data distribution, which fundamentally limits predictive performance. This review paper examines formal methodologies that address data-limited regimes through two complementary approaches: quantifying epistemic uncertainty and mitigating data scarcity via synthetic data augmentation. We begin by reviewing generalized Bayesian learning frameworks that characterize epistemic uncertainty through generalized posteriors in the model parameter space, as well as ``post-Bayes'' learning frameworks. We continue by presenting information-theoretic generalization bounds that formalize the relationship between training data quantity and predictive uncertainty, providing a theoretical justification for generalized Bayesian learning. Moving beyond methods with asymptotic statistical validity, we survey uncertainty quantification methods that provide finite-sample statistical guarantees, including conformal prediction and conformal risk control. Finally, we examine recent advances in data efficiency by combining limited labeled data with abundant model predictions or synthetic data. Throughout, we take an information-theoretic perspective, highlighting the role of information measures in quantifying the impact of data scarcity.
CARD: Correlation Aware Restoration with Diffusion
Venue: arXiv cs.CV 2025
Year: 2025

Denoising diffusion models have achieved state-of-the-art performance in image restoration by modeling the process as sequential denoising steps. However, most approaches assume independent and identically distributed (i.i.d.) Gaussian noise, while real-world sensors often exhibit spatially correlated noise due to readout mechanisms, limiting their practical effectiveness. We introduce Correlation Aware Restoration with Diffusion (CARD), a training-free extension of DDRM that explicitly handles correlated Gaussian noise. CARD first whitens the noisy observation, which converts the noise into an i.i.d. form. Then, the diffusion restoration steps are replaced with noise-whitened updates, which inherits DDRM's closed-form sampling efficiency while now being able to handle correlated noise. To emphasize the importance of addressing correlated noise, we contribute CIN-D, a novel correlated noise dataset captured across diverse illumination conditions to evaluate restoration methods on real rolling-shutter sensor noise. This dataset fills a critical gap in the literature for experimental evaluation with real-world correlated noise. Experiments on standard benchmarks with synthetic correlated noise and on CIN-D demonstrate that CARD consistently outperforms existing methods across denoising, deblurring, and super-resolution tasks.